On minimap2 github (https://github.com/lh3/minimap2) it says :
For long RNA-seq reads, minimap2 may produce chimeric alignments potentially caused by gene fusions/structural variations or by an intron longer than the max intron length -G (200k by default). For now, it is not recommended to apply an excessively large -G as this slows down minimap2 and sometimes leads to false alignments.
How can I extract such chimeric reads ? Are these only cis-fusions (on the same chromosome) or also trans fusions (different chromosomes) ? Is there a way to tune the chimeric detection ?